In the test .vcf there is only one sample (i.e. Pool1), but it could contain information about more samples (e.g. parent genotyping or other pools data).
If your have a .vcf file with information from multiple experiments, this fields becomes useful.

You can see an example downloading this file. We normally use alt counts based on the
assumption that that the reference used for the DNA mapping is the inferior parent. Therefore, alt counts are the supperior parent counts
at the marker sites.

Input Experimental Information - Step 3: Alpha/Beta ratios

The black line is the background beta distribution detected from the data.

Select several sets of parameters to run the Hidden Markov Model with:α= 5, β=1 is meant to have high sensitivity.α=10, β=1 is meant to be a middle ground between sensitivity and specificity.α=30, β=1 is meant to have high specificty.

The ratio between alfa and beta: You can run the tool for different ratio's. The higher alfa becomes, the more stringent the
search i.e.
the more the effect of the QTL needs to be (the more overrepresented the number of superior allele counts versus the total number of
allele counts at a marker site. Regions that will be detected with the most stringent setting will also be detected with
less stringent settings. The more stringent the setting at which a region can still be detected, the more reliably the QTL association
is. Note also that increasing the stringency of the setting allows to decrease the region that associates: because of LD,
the number of markers that correlate with the truly associating marker site decreases with the distance from the truly associating
site. The more stringent the setting the less 'correlating markers' still meet the criteria to be selected.

The users should select sets of parameters that produce distributions that intersect the neutral variant allele frequency distribution.
Distributions with bigger intersects to the neutral variant allele frequency distribution are more sensitive.
Distributions more skewed to the right and farther from the neutral variant allele frequency distribution are more stringent.
Check these simulations results (here and
here) for more information about the performance
of the methods with different parameters and scenarios.

Download test data:

You can use a standard .vcf file and enter the name of the sample that want to analysed. If the name is empty, the first sample will be analysed.

A file like this can be generated with NGSEP or GATK. A tutorial for NGSEP can be found here.

You can see an example downloading this file. We normally use alt counts based on the
assumption that that the reference used for the DNA mapping is the inferior parent. Therefore, alt counts are the supperior parent counts
at the marker sites.